Alignments for a candidate for astA in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for astA in Paraburkholderia bryophila 376MFSha3.1

Align Arginine N-succinyltransferase; AST; AOST; EC 2.3.1.109 (characterized)
to candidate H281DRAFT_06480 H281DRAFT_06480 arginine succinyltransferase

Query= SwissProt::P0AE37
         (344 letters)



>FitnessBrowser__Burk376:H281DRAFT_06480
          Length = 345

 Score =  320 bits (820), Expect = 3e-92
 Identities = 161/340 (47%), Positives = 225/340 (66%), Gaps = 3/340 (0%)

Query: 1   MMVIRPVERSDVSALMQLASKTGGGLTSLPANEATLSARIERAIKTWQGELPKSEQGYVF 60
           M+V+R V+R DV ALM+LA +TG GLT+   +   L+AR+ERA +T + +    E GY F
Sbjct: 1   MIVVRVVQRGDVDALMRLAQETGPGLTTFKPDRDALAARVERARRTMEDKAEPHEAGYFF 60

Query: 61  VLEDSETGTVAGICAIEVAVGLNDPWYNYRVGTLVHASKELNVYNALPTLFLSNDHTGSS 120
           V+ED+ TG VAG+C IE AVGL  P+YNYRV T+VHAS++L ++  +  L +S+D TG +
Sbjct: 61  VMEDTATGDVAGVCGIETAVGLQQPFYNYRVSTVVHASQDLGIWTRMRALNISHDLTGYA 120

Query: 121 ELCTLFLDPDWRKEGNGYLLSKSRFMFMAAFRDKFNDKVVAEMRGVIDEHGYSPFWQSLG 180
           E+C+LFL P +R  G G LLS+SRFMF+A FR++F  ++ AE+RG  D  G SPFW+++G
Sbjct: 121 EVCSLFLSPRYRTSGVGGLLSRSRFMFLAQFRERFPQRLCAELRGHFDAEGTSPFWRAVG 180

Query: 181 KRFFSMDFSRADFLCGTGQKAFIAELMPKHPIYTHFLSQEAQDVIGQVHPQTAPARAVLE 240
             F+ +DF+ AD+L   G+KAF+AELMP++P+Y   L QEAQ+ +G  H  T PAR +LE
Sbjct: 181 SHFYQIDFNAADYLSSHGRKAFLAELMPRYPVYVELLPQEAQECVGLTHNDTIPARRMLE 240

Query: 241 KEGFRYRNYIDIFDGGPTLECDIDRVRAIRKSRLVEVAEGQPAQG---DFPACLVANENY 297
            EG RY N++DIFD GP LEC I  +R +R+S LV V      +G   D P  +V+N + 
Sbjct: 241 AEGLRYENHVDIFDAGPVLECHISDLRTVRESVLVPVEIADVPEGAAQDAPRSMVSNTSL 300

Query: 298 HHFRVVLVRTDPATERLILTAAQLDALKCHAGDRVRLVRL 337
             FRV +    P      + A +  AL   AGD VR++ L
Sbjct: 301 GDFRVGVAAGVPQDGVFRMNATEAAALGVKAGDPVRVLAL 340


Lambda     K      H
   0.321    0.136    0.411 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 351
Number of extensions: 9
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 344
Length of database: 345
Length adjustment: 29
Effective length of query: 315
Effective length of database: 316
Effective search space:    99540
Effective search space used:    99540
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 49 (23.5 bits)

Align candidate H281DRAFT_06480 H281DRAFT_06480 (arginine succinyltransferase)
to HMM TIGR03244 (astA: arginine N-succinyltransferase (EC 2.3.1.109))

# hmmsearch :: search profile(s) against a sequence database
# HMMER 3.3.1 (Jul 2020); http://hmmer.org/
# Copyright (C) 2020 Howard Hughes Medical Institute.
# Freely distributed under the BSD open source license.
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
# query HMM file:                  ../tmp/path.carbon/TIGR03244.hmm
# target sequence database:        /tmp/gapView.13199.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR03244  [M=336]
Accession:   TIGR03244
Description: arg_catab_AstA: arginine N-succinyltransferase
Scores for complete sequences (score includes all domains):
   --- full sequence ---   --- best 1 domain ---    -#dom-
    E-value  score  bias    E-value  score  bias    exp  N  Sequence                                    Description
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
     2e-149  482.9   0.0   2.3e-149  482.7   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_06480  H281DRAFT_06480 arginine succiny


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_06480  H281DRAFT_06480 arginine succinyltransferase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  482.7   0.0  2.3e-149  2.3e-149       1     336 []       3     340 ..       3     340 .. 0.98

  Alignments for each domain:
  == domain 1  score: 482.7 bits;  conditional E-value: 2.3e-149
                                    TIGR03244   1 ivrpvktsdldallelakeaGvGltslpaneellekrieraeksfageleraeegylfvledtetg 66 
                                                  +vr+v++ d+dal++la+e+G Glt+++ ++++l++r+era++++++++e+ e+gy+fv+edt+tg
  lcl|FitnessBrowser__Burk376:H281DRAFT_06480   3 VVRVVQRGDVDALMRLAQETGPGLTTFKPDRDALAARVERARRTMEDKAEPHEAGYFFVMEDTATG 68 
                                                  79**************************************************************** PP

                                    TIGR03244  67 kvvGvsaieaavGleepfynyrvgkvvhaskelniykkletlflsndltgaselCtlfldeeyrke 132
                                                  +v+Gv++ie+avGl++pfynyrv++vvhas++l+i++++ +l++s+dltg++e+C+lfl+++yr++
  lcl|FitnessBrowser__Burk376:H281DRAFT_06480  69 DVAGVCGIETAVGLQQPFYNYRVSTVVHASQDLGIWTRMRALNISHDLTGYAEVCSLFLSPRYRTS 134
                                                  ****************************************************************** PP

                                    TIGR03244 133 lnGkllskarflflaefkerfskkiiaemrGvsdeeGrsPfWealgkkffsldfskadylsgiGkk 198
                                                   +G lls++rf+fla+f+erf ++++ae+rG++d eG+sPfW+a+g++f+++df++adyls++G+k
  lcl|FitnessBrowser__Burk376:H281DRAFT_06480 135 GVGGLLSRSRFMFLAQFRERFPQRLCAELRGHFDAEGTSPFWRAVGSHFYQIDFNAADYLSSHGRK 200
                                                  ****************************************************************** PP

                                    TIGR03244 199 afiaelmPkfPiyvdllskeaqdvigkvhektkPalalleseGlryqgyvdifdaGptleaevaki 264
                                                  af+aelmP++P+yv+ll++eaq+ +g +h++t Pa+++le+eGlry+++vdifdaGp+le++++++
  lcl|FitnessBrowser__Burk376:H281DRAFT_06480 201 AFLAELMPRYPVYVELLPQEAQECVGLTHNDTIPARRMLEAEGLRYENHVDIFDAGPVLECHISDL 266
                                                  ****************************************************************** PP

                                    TIGR03244 265 ravresklvevavaes..aaedeaepylvanekledfrvvlvessldaeelvlsaeeakalkveeG 328
                                                  r+vres lv+v++a++   a ++a++++v+n++l dfrv ++    + + + ++a+ea+al v++G
  lcl|FitnessBrowser__Burk376:H281DRAFT_06480 267 RTVRESVLVPVEIADVpeGAAQDAPRSMVSNTSLGDFRVGVAAGVPQDGVFRMNATEAAALGVKAG 332
                                                  **********999876223456699***************************************** PP

                                    TIGR03244 329 dkvrvval 336
                                                  d vrv+al
  lcl|FitnessBrowser__Burk376:H281DRAFT_06480 333 DPVRVLAL 340
                                                  *****986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (336 nodes)
Target sequences:                          1  (345 residues searched)
Passed MSV filter:                         1  (1); expected 0.0 (0.02)
Passed bias filter:                        1  (1); expected 0.0 (0.02)
Passed Vit filter:                         1  (1); expected 0.0 (0.001)
Passed Fwd filter:                         1  (1); expected 0.0 (1e-05)
Initial search space (Z):                  1  [actual number of targets]
Domain search space  (domZ):               1  [number of targets reported over threshold]
# CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 11.89
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources